Ms Sujatha is only the second recipient of the prize
Ramdorai Sujatha, from the Tata Institute of Fundamental Research in Mumbai, picked up up the award at a ceremony in Trieste, Italy.
The prize was set up last year, so 44-year-old Professor Sujatha is the second recipient of the $10,000 award.
The award is named after the Indian mathematics genius Srinivasa Ramanujan.
It is to be awarded annually to a mathematician under 45 from a developing country.
This year's recipient was honoured for her work on the "arithmetic of algebraic varieties" and her substantial contributions to a mathematical framework known as Iwasawa theory.
"In the last few years there have been a flurry of various prizes instituted for mathematical research, but none that was addressed to support mathematics in developing nations," said Professor Sujatha.
"It is an important recognition and serves well to integrate mathematics globally. It will certainly inspire working mathematicians in the developing nations."
She said that women in developing countries could face career obstacles, but that she had encountered none herself.
But she added: "It is true that the scientific policies could be shaped towards making them sensitive to the problems of women and this is happening to a certain extent."
She was presented with the prize by Professor Lennart Carleson in a ceremony at the Abdus Salam International Centre for Theoretical Physics (ICTP) in Trieste, Italy.
Professor Carleson, of the Royal Institute of Technology, Sweden, was this year's winner of the Abel Prize, which has been dubbed the "Nobel prize for maths".
The Nobel Foundation currently has no award for mathematics, and the Abel Prize was set up to fill this vacuum.
The Ramanujan prize, meanwhile, was established by the ICTP as part of its mandate to strengthen science in developing countries.
"Scientific development is part of the overall development and the increased interconnectedness of the world today implies that it is dangerous for all of us to leave any part of it too far behind," said KR Sreenivasan, the ICTP's director.The ICTP operates under the aegis of two UN agencies: the United Nations Educational, Scientific and Cultural Organization (Unesco) and the International Atomic Energy Agency (IAEA).